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Phylogenomics: a Genome Level Approach to Assembling the Bacterial Branches of the Tree of Life

Phylogenomics: a Genome Level Approach to Assembling the Bacterial Branches of the Tree of Life

Phylogenomics: A Level Approach to Assembling the Bacterial Branches of the Tree of

Jonathan A. Eisen Naomi Ward Karen E. Nelson Frank T. Robb Jonathan H. Badger QuickTimeª and a TIFF (LZW) decompressor James Sakwa are needed to see this picture. Martin Wu Dongying Wu Kevin Penn Elizabeth M. O’Connor Julie Enticknap Tim Steppe

http://www.tigr.org/tol

TIGTIGRR Background I: rRNA Tree

• Phenotype not very useful for bacterial phylogeny

• Most molecular studies

QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. based on 16s rRNA sequence analysis

• Studies of other do not always agree with rRNA, especially for deep branches TIGTIGRR Background II: Most Have Never Been Cultured

• Microscopic and molecular studies show that <1% of the microbes in most environments have been grown in pure culture • True in terms of #s and phylogenetic diversity • This means we know little about their biology

TIGTIGRR Background III: Has Revolutionized Bacteriology

• Predictions of biology • Drug design, vaccine development • Functional genomic studies • Evolutionary reconstructions – Whole genome phylogeny – Lateral transfer – Population genomics

TIGTIGRR Biased Sampling of Bacterial

Hugenholtz 2002 TIGTIGRR Automated Whole Genome Phylogeny TIGTIGRR TIGR Tree of Life Project

• Major goal – Increase phylogenetic diversity of genome sequences • Three sub-goals – Resolve relationships among the phyla – Launch experimental studies of these phyla – Inform environmental studies of uncultured microbes • The Players – TIGR (Jonathan Eisen, Naomi Ward, Karen Nelson et al.) – COMB (Frank Robb et al.)

TIGTIGRR TM6 OS-K Termite Group OP8 CFB Chlorobi Marine GroupA WS3 Gemmimonas This project OP9 Published Synergistes In progress Deferribacteres Chrysiogenetes Uncultured lineage NKB19 OP3 Spriochaetes 0.1 Coprothermobacter OP10 TM7 - Dictyoglomus Aquificacae Tree based on Hugenholtz (2002) OP1 with some TIGTIGRR OP11 modifications. Genome Sequencing Progress

Phylum Species selected Growth, Libraries Shotgun Estimated # of Auto- DNA Coverage Genome Contigs Annotated isolation Size (Mb) Chrysiogenes Chrysiogenes arsenatis + + 4x 2.5 155 +

Coprothermobacter Coprothermobacter proteolyticus (CP) + + 8x 1.38 3 +

Dictyoglomi Dictyoglomus thermophilum (DT) + + 8x 2.0 9 +

Thermodesulfobacteria Thermodesulfobacterium commune (TC) + + 8x 1.78 26 +

Nitrospirae Thermodesulfovibrio yellowstonii (TY) + + 8x 1.98 27 +

Thermomicrobia Thermomicrobium roseum + + 8x 3.4 82 +

Deferribacteres Selecting from + In Deferribacter thermophilus, progress Geovibrio thiophilus, Flexistipes sinusarabici Synergistes Selecting from + In Synergistes jonesii, progress Aminobacter colombiense, Thermanaerovibrio acidaminovorans, Aminomonas paucivorans , Dethiosulfovibrio peptidovorans

Type Strain or Species Selected When Possible TIGTIGRR Goal I:

Relationships Among Phyla

TIGTIGRR Concatenated Alignment ML Tree

TIGTIGRR Proteobacteria

TIGTIGRR Green Non Bacteria

TIGTIGRR Goal II:

Biology of These Phyla

TIGTIGRR QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture.

TIGTIGRR Goal III:

Uncultured Microbes

TIGTIGRR Key Issues in Uncultured Microbes

• Questions – 1. Who is out there? – 2. What are they doing? – 3. Need to connect 1 and 2. • Answers – 1. Phylogenetic anchors – 2. Genomics – 3. Linking anchors to genomics contigs

TIGTIGRR Phylogenetic Anchors and the Sargasso Sea Shotgun Sequencing

Warner BBrothers, Inc. shotgun

sequence

TIGTIGRR rRNA as a Phylogenetic Anchor

TIGTIGRR Venter et al., 2004 Shotgun Sequencing Allows Use of Alternative Anchors (e.g., RecA)

TIGTIGRR Venter et al., 2004 Biased Sampling of Bacterial Genomes

Hugenholtz 2002 TIGTIGRR Our Tree of Life Genomes Allow Anchoring of 100s of clones from Yellowstone Mats

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TIGTIGRR Tree of GYOAP59TF

TIGTIGRR Blast of GYOAP59TF

>ORF02612-TG_gtr_857 rho transcription termination factor Rho {Thermomicrobium_roseum_DSM5159} Length = 426

Score = 1177 (419.4 bits), Expect = 2.9e-119, P = 2.9e-119 Identities = 232/232 (100%), Positives = 232/232 (100%)

Query: 1 VAPIGRGQRGLIVSPPKAGKTVLLKHIANGITTNYKDIHLIVLLIGERPEEVTDMRRSVD 60 VAPIGRGQRGLIVSPPKAGKTVLLKHIANGITTNYKDIHLIVLLIGERPEEVTDMRRSVD Sbjct: 191 VAPIGRGQRGLIVSPPKAGKTVLLKHIANGITTNYKDIHLIVLLIGERPEEVTDMRRSVD 250

Query: 61 GEVISSTFDEPVEDHIRVAEMTLERAKRLVECGMDVVILLDSITRLARAYNLSVPPSGRT 120 GEVISSTFDEPVEDHIRVAEMTLERAKRLVECGMDVVILLDSITRLARAYNLSVPPSGRT Sbjct: 251 GEVISSTFDEPVEDHIRVAEMTLERAKRLVECGMDVVILLDSITRLARAYNLSVPPSGRT 310

Query: 121 LSGGIDPVALYPPKRFFGAARNIEGGGSLTIIATCLVDTGSRMDDVIYEEFKGTGNMELH 180 LSGGIDPVALYPPKRFFGAARNIEGGGSLTIIATCLVDTGSRMDDVIYEEFKGTGNMELH Sbjct: 311 LSGGIDPVALYPPKRFFGAARNIEGGGSLTIIATCLVDTGSRMDDVIYEEFKGTGNMELH 370

Query: 181 LDRKLAERRIFPAIDIQRSGTRREELLLDEQTLRQVWTMRRMVSMLGGTDGT 232 LDRKLAERRIFPAIDIQRSGTRREELLLDEQTLRQVWTMRRMVSMLGGTDGT Sbjct: 371 LDRKLAERRIFPAIDIQRSGTRREELLLDEQTLRQVWTMRRMVSMLGGTDGT 422

TIGTIGRR Broader Impact

• Genome sequence data released to TIGR web site • Genome Users Workshop to be held at TIGR in 2005 • Project used as model for evolution teaching in talks to HHMI, MD Science Teachers Assocation, and Montgomery County high school science teachers • Project promoted to public through radio and print media

TIGTIGRR Training

• Student involvement – Kevin Penn, technician at TIGR – Temylope Adeyefa-Olasupo, U. Md Undergrad working at COMB – Rebecca Brocato, high school intern, COMB – Joseph Wister, TIGR Summer Fellow with Karen Nelson – Ryan Corces-Zimmerman, high school intern working at TIGR • Teaching using this project – MBL Molecular Evolution Workshop – MBL Genomics Workshop TIGTIG–RRJackson Lab Genomics Workshop Future Issues

• New estimates suggests > 100 • Someone needs to cover Archaeal diversity • Need DNA repository

TIGTIGRR

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